Question

Change sign from Granges scores to visualize negative strand data

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ferbecneu • 0

@ferbecneu-16188

Last seen 3.5 years ago

Hello I wish to add minus signs in my granges scores. These scores come from a Gro-seq bigwig and they are counts from the negative strand however they come as positive values. I want to make them negative so that I can visualize the signal together with positive strand tracks in the genome browser. Can this be done in granges? Thank you very much!

granges rtracklayer • 1.1k views

ADD COMMENT • link updated 5.2 years ago by James W. MacDonald 65k • written 5.2 years ago by ferbecneu • 0

score 0 · Answer 1 · 2019-02-13

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 8 hours ago

United States

> z <- GRanges(rep("chr1", 10), IRanges(1:10, 31:40))
> z
GRanges object with 10 ranges and 0 metadata columns:
       seqnames    ranges strand
          <Rle> <IRanges>  <Rle>
   [1]     chr1      1-31      *
   [2]     chr1      2-32      *
   [3]     chr1      3-33      *
   [4]     chr1      4-34      *
   [5]     chr1      5-35      *
   [6]     chr1      6-36      *
   [7]     chr1      7-37      *
   [8]     chr1      8-38      *
   [9]     chr1      9-39      *
  [10]     chr1     10-40      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> strand(z) <- rep("-", 10)
> z
GRanges object with 10 ranges and 0 metadata columns:
       seqnames    ranges strand
          <Rle> <IRanges>  <Rle>
   [1]     chr1      1-31      -
   [2]     chr1      2-32      -
   [3]     chr1      3-33      -
   [4]     chr1      4-34      -
   [5]     chr1      5-35      -
   [6]     chr1      6-36      -
   [7]     chr1      7-37      -
   [8]     chr1      8-38      -
   [9]     chr1      9-39      -
  [10]     chr1     10-40      -
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

ADD COMMENT • link 5.2 years ago James W. MacDonald 65k

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Or maybe you mean something in the mcols slot?

> mcols(z)$scores <- runif(10)
> z
GRanges object with 10 ranges and 1 metadata column:
       seqnames    ranges strand |            scores
          <Rle> <IRanges>  <Rle> |         <numeric>
   [1]     chr1      1-31      - | 0.781348916934803
   [2]     chr1      2-32      - | 0.689271170645952
   [3]     chr1      3-33      - |  0.50072684045881
   [4]     chr1      4-34      - | 0.113180985907093
   [5]     chr1      5-35      - | 0.495131695410237
   [6]     chr1      6-36      - | 0.868058342020959
   [7]     chr1      7-37      - | 0.615485859103501
   [8]     chr1      8-38      - | 0.418453785357997
   [9]     chr1      9-39      - | 0.155853351112455
  [10]     chr1     10-40      - | 0.831564369145781
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> mcols(z)$scores <- -1*mcols(z)$scores
> z
GRanges object with 10 ranges and 1 metadata column:
       seqnames    ranges strand |             scores
          <Rle> <IRanges>  <Rle> |          <numeric>
   [1]     chr1      1-31      - | -0.781348916934803
   [2]     chr1      2-32      - | -0.689271170645952
   [3]     chr1      3-33      - |  -0.50072684045881
   [4]     chr1      4-34      - | -0.113180985907093
   [5]     chr1      5-35      - | -0.495131695410237
   [6]     chr1      6-36      - | -0.868058342020959
   [7]     chr1      7-37      - | -0.615485859103501
   [8]     chr1      8-38      - | -0.418453785357997
   [9]     chr1      9-39      - | -0.155853351112455
  [10]     chr1     10-40      - | -0.831564369145781
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
>

ADD REPLY • link 5.2 years ago James W. MacDonald 65k

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It was the second scenario. Thank you very much!

ADD REPLY • link 5.2 years ago ferbecneu • 0

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It was the second scenario. Thank you very much!

ADD REPLY • link 5.2 years ago ferbecneu • 0